How do I prevent Blender from randomly duplicating items?
Modifiers are in wrong order. Move Smoke modifier down in the stack so Particle system would be first. At least i think this is what you are trying to achieve. 

Oh and it ain't random duplicating. You have "Smoke adaptive Domain" checked on Domain Smoke properties and because modifiers were in wrong order, it looked like there is duplicated domain as it should normally stay inside the original domain.

EDIT: Well that particle system seemed bit complicated for me to fast figure out how to make that more "firebending" style you wanted. But here is idea for you how to do it easier without using particle system. Added another domain, sphere and wind. might be more better way to do this, but this is what i would use